TSPYL5

TSPY like 5

Basic information

Region (hg38): 8:97273488-97277928

Links

ENSG00000180543 ∙ NCBI:85453 ∙ OMIM:614721 ∙ HGNC:29367 ∙ Uniprot:Q86VY4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSPYL5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPYL5 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in TSPYL5

This is a list of pathogenic ClinVar variants found in the TSPYL5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-97276608-C-T		not specified	Uncertain significance (Jun 24, 2022)
8-97276683-G-A		not specified	Uncertain significance (Jun 06, 2023)
8-97276689-C-T		not specified	Uncertain significance (Feb 13, 2024)
8-97276803-G-A		not specified	Uncertain significance (Feb 11, 2022)
8-97276825-G-T		not specified	Uncertain significance (Mar 20, 2024)
8-97276868-G-A		not specified	Uncertain significance (Feb 28, 2023)
8-97277026-T-C			Likely benign (Jul 01, 2023)
8-97277031-C-G		not specified	Uncertain significance (Mar 28, 2024)
8-97277085-G-T		not specified	Uncertain significance (Jan 19, 2024)
8-97277104-A-C		not specified	Uncertain significance (May 11, 2022)
8-97277159-T-C		not specified	Uncertain significance (Oct 13, 2023)
8-97277243-C-T		not specified	Uncertain significance (Feb 05, 2024)
8-97277252-G-A		not specified	Uncertain significance (May 18, 2022)
8-97277270-C-A		not specified	Uncertain significance (Jun 03, 2024)
8-97277328-C-A		not specified	Uncertain significance (Mar 25, 2024)
8-97277340-T-C		not specified	Uncertain significance (Oct 06, 2021)
8-97277396-G-C		not specified	Uncertain significance (Oct 12, 2022)
8-97277405-T-C		not specified	Uncertain significance (Jul 19, 2022)
8-97277409-C-G		not specified	Uncertain significance (Nov 12, 2021)
8-97277436-G-C		not specified	Uncertain significance (Sep 16, 2021)
8-97277438-G-A			Likely benign (Dec 13, 2017)
8-97277625-C-T		not specified	Uncertain significance (Mar 25, 2022)
8-97277631-G-A		not specified	Uncertain significance (Jan 24, 2023)
8-97277778-C-G		not specified	Uncertain significance (Jun 24, 2022)
8-97277813-G-A		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPYL5	protein_coding	protein_coding	ENST00000322128	1	4460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.849	0.150	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	180	233	0.774	0.0000147	2651
Missense in Polyphen		46	75.288	0.61099		925
Synonymous	-0.728	110	101	1.09	0.00000668	857
Loss of Function	2.73	1	10.6	0.0944	5.93e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in modulation of cell growth and cellular response to gamma radiation probably via regulation of the Akt signaling pathway. Involved in regulation of p53/TP53. Suppresses p53/TP53 protein levels and promotes its ubiquitination; the function is dependent on USP7 and independent on MDM2. Proposed to displace p53/TP53 from interaction with USP7. {ECO:0000269|PubMed:20079711, ECO:0000269|PubMed:21170034}.

Recessive Scores

• pRec: 0.119

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.181
• hipred: N
• hipred_score: 0.431
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.312

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tspyl5

Gene ontology

• Biological process: nucleosome assembly;positive regulation of cell population proliferation;positive regulation of protein ubiquitination;regulation of growth;positive regulation of protein kinase B signaling;cellular response to gamma radiation
• Cellular component: nucleus
• Molecular function: protein binding